Abstract: In order to study the effects of CM-microbial organic fertilizer on tobacco disease resistance, yield and inner quality of tobacco leaf, we carried out field experiments in Sichuan Province. The results showed that: by the application of CM-microbial organic fertilizer, the growth and quality of tobacco were improved, yield per unit and mass area ratio were increased, the incidence of diseases was decreased, the contents of total sugar and reducing sugar were slightly reduced and the contents of total alkaloid, sugar-nicotine ratio, the ratio of nitrogen to nicotine were obviously lowered, closer to the coordination requirements for routine chemical compositions of flue-cured tobacco, and smoking quality was also improved. When CM-microbial organic fertilizer was applied in soil, the growth, disease resistance, yield per unit, mass area ratio and inner quality of flue-cured tobacco were improved, at the same time chemical fertilizers application was reduced.